InStrain

InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification

Source code is available on GitHub.

Publication is available on bioRxiv

See links to the left for Installation instructions

Comments and suggestions can be sent to Matt Olm and/or Alex Crits-Christoph

Bugs reports and feature requests can be submitted through GitHub.

Contents

• Installation
  • Installation
  • Docker image
  • Quick Start
• Overview and FAQ
  • Overview
  • FAQ (Frequently asked questions)
  • Glossary of terms used in inStrain
• Tutorial
  • Quick Start
  • Running inStrain with custom genomes
  • Running inStrain with public reference genomes
• Program documentation
  • Preparing input
  • Module descriptions
• Example output and explanations
  • inStrain profile
  • inStrain compare
  • inStrain profile_genes
  • inStrain genome_wide
  • inStrain plot
• Advanced use
  • Adjusting parameters
  • Accessing raw data
  • A note for programmers